Starting phenix.real_space_refine on Thu Jun 19 14:34:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0l_39707/06_2025/8z0l_39707_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0l_39707/06_2025/8z0l_39707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0l_39707/06_2025/8z0l_39707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0l_39707/06_2025/8z0l_39707.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0l_39707/06_2025/8z0l_39707_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0l_39707/06_2025/8z0l_39707_neut.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 110 5.16 5 C 14214 2.51 5 N 3812 2.21 5 O 4625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22858 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2632 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 309} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2604 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 307} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "C" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "D" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2581 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1968 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 246} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2422 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 16, 'TRANS': 305} Chain breaks: 3 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2430 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2339 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 648 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "J" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 148 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "L" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1249 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 12, 'rna3p_pur': 21, 'rna3p_pyr': 12} Link IDs: {'rna2p': 25, 'rna3p': 32} Chain breaks: 1 Chain: "M" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1261 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 57 Time building chain proxies: 15.51, per 1000 atoms: 0.68 Number of scatterers: 22858 At special positions: 0 Unit cell: (108.75, 149.25, 161.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 110 16.00 P 97 15.00 O 4625 8.00 N 3812 7.00 C 14214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 2.8 seconds 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5018 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 43 sheets defined 30.0% alpha, 24.3% beta 20 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 8.14 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.636A pdb=" N ARG A 40 " --> pdb=" O PHE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.615A pdb=" N GLU A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.777A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.748A pdb=" N ALA A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.702A pdb=" N GLN A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.751A pdb=" N ILE A 254 " --> pdb=" O HIS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.505A pdb=" N LEU A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'B' and resid 63 through 71 removed outlier: 3.706A pdb=" N GLU B 68 " --> pdb=" O PRO B 64 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.721A pdb=" N ARG B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.579A pdb=" N ALA B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.752A pdb=" N GLN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 removed outlier: 3.509A pdb=" N ILE B 254 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 302 removed outlier: 3.545A pdb=" N ASP B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.517A pdb=" N LYS C 39 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG C 40 " --> pdb=" O PHE C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 63 through 71 removed outlier: 3.731A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 removed outlier: 3.558A pdb=" N ARG C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.729A pdb=" N ALA C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 202 removed outlier: 4.132A pdb=" N GLN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.649A pdb=" N ILE C 254 " --> pdb=" O HIS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 Processing helix chain 'C' and resid 312 through 326 removed outlier: 3.646A pdb=" N TYR C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 321 " --> pdb=" O HIS C 317 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.032A pdb=" N ARG D 40 " --> pdb=" O PHE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 70 removed outlier: 3.620A pdb=" N LYS D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.735A pdb=" N ALA D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.722A pdb=" N GLN D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 removed outlier: 3.701A pdb=" N ILE D 254 " --> pdb=" O HIS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 302 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 27 through 43 removed outlier: 3.864A pdb=" N PHE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 removed outlier: 3.546A pdb=" N CYS E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 168 Processing helix chain 'E' and resid 173 through 185 Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'F' and resid 19 through 29 removed outlier: 3.540A pdb=" N PHE F 28 " --> pdb=" O ILE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 93 Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 112 through 123 removed outlier: 3.861A pdb=" N GLU F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU F 120 " --> pdb=" O HIS F 116 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR F 122 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP F 123 " --> pdb=" O GLU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 131 through 133 No H-bonds generated for 'chain 'F' and resid 131 through 133' Processing helix chain 'F' and resid 167 through 177 Processing helix chain 'F' and resid 191 through 199 removed outlier: 3.891A pdb=" N GLY F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 223 through 228 Processing helix chain 'F' and resid 229 through 231 No H-bonds generated for 'chain 'F' and resid 229 through 231' Processing helix chain 'F' and resid 255 through 266 Processing helix chain 'F' and resid 273 through 277 removed outlier: 3.682A pdb=" N ARG F 277 " --> pdb=" O ARG F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 293 removed outlier: 3.530A pdb=" N LEU F 289 " --> pdb=" O VAL F 285 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 320 removed outlier: 3.554A pdb=" N ASN F 319 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET F 320 " --> pdb=" O ILE F 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 316 through 320' Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.503A pdb=" N VAL F 331 " --> pdb=" O HIS F 327 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 333 " --> pdb=" O GLU F 329 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA F 336 " --> pdb=" O THR F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 40 removed outlier: 3.847A pdb=" N ARG G 40 " --> pdb=" O PHE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.843A pdb=" N ALA G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 202 removed outlier: 3.729A pdb=" N GLN G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.571A pdb=" N ILE G 254 " --> pdb=" O HIS G 250 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA G 257 " --> pdb=" O LYS G 253 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU G 258 " --> pdb=" O ILE G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 303 Processing helix chain 'G' and resid 312 through 324 Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 186 through 201 removed outlier: 3.719A pdb=" N ASN H 190 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 259 removed outlier: 3.603A pdb=" N ILE H 254 " --> pdb=" O HIS H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 removed outlier: 3.526A pdb=" N MET H 304 " --> pdb=" O LEU H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 326 removed outlier: 3.904A pdb=" N ALA H 321 " --> pdb=" O HIS H 317 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 23 removed outlier: 3.582A pdb=" N ILE M 19 " --> pdb=" O SER M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 35 removed outlier: 3.664A pdb=" N VAL M 27 " --> pdb=" O ASP M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 71 Processing helix chain 'M' and resid 72 through 77 removed outlier: 3.605A pdb=" N LEU M 77 " --> pdb=" O LEU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 118 removed outlier: 3.785A pdb=" N ARG M 114 " --> pdb=" O THR M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 139 removed outlier: 3.534A pdb=" N HIS M 130 " --> pdb=" O PRO M 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 109 removed outlier: 6.687A pdb=" N SER A 20 " --> pdb=" O TYR A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.544A pdb=" N LYS A 31 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 57 Processing sheet with id=AA5, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 109 removed outlier: 3.505A pdb=" N SER B 108 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AA9, first strand: chain 'B' and resid 50 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AB2, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AB3, first strand: chain 'C' and resid 106 through 108 removed outlier: 3.744A pdb=" N SER C 108 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AB6, first strand: chain 'C' and resid 50 through 57 Processing sheet with id=AB7, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AB9, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AC2, first strand: chain 'D' and resid 50 through 56 Processing sheet with id=AC3, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC4, first strand: chain 'D' and resid 260 through 262 Processing sheet with id=AC5, first strand: chain 'D' and resid 282 through 283 removed outlier: 3.846A pdb=" N ALA D 283 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE D 288 " --> pdb=" O ALA D 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 137 through 138 removed outlier: 5.136A pdb=" N TYR E 4 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL E 111 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU E 6 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU E 109 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU E 8 " --> pdb=" O PHE E 107 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE E 107 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN E 14 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE E 101 " --> pdb=" O ASN E 14 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU E 60 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER E 106 " --> pdb=" O PHE E 58 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N PHE E 58 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU E 108 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU E 56 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLU E 110 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL E 54 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLU E 112 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASN E 52 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 14.492A pdb=" N VAL E 54 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N LEU E 161 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU E 56 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE E 216 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA E 197 " --> pdb=" O PHE E 216 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU E 218 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE E 195 " --> pdb=" O GLU E 218 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 220 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL E 193 " --> pdb=" O CYS E 251 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 143 through 146 removed outlier: 3.973A pdb=" N LYS E 143 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TYR E 4 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL E 111 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU E 6 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU E 109 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU E 8 " --> pdb=" O PHE E 107 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE E 107 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN E 14 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE E 101 " --> pdb=" O ASN E 14 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU E 60 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER E 106 " --> pdb=" O PHE E 58 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N PHE E 58 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU E 108 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU E 56 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLU E 110 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL E 54 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLU E 112 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASN E 52 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 14.492A pdb=" N VAL E 54 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N LEU E 161 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU E 56 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASP E 213 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N SER F 162 " --> pdb=" O ASP E 213 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS E 215 " --> pdb=" O SER F 162 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS F 148 " --> pdb=" O ILE F 163 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 22 through 24 removed outlier: 6.276A pdb=" N VAL E 23 " --> pdb=" O ALA F 214 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 Processing sheet with id=AD1, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD2, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AD3, first strand: chain 'F' and resid 301 through 304 Processing sheet with id=AD4, first strand: chain 'G' and resid 106 through 109 removed outlier: 3.668A pdb=" N SER G 108 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=AD6, first strand: chain 'G' and resid 45 through 46 Processing sheet with id=AD7, first strand: chain 'G' and resid 50 through 53 Processing sheet with id=AD8, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AD9, first strand: chain 'G' and resid 260 through 262 Processing sheet with id=AE1, first strand: chain 'H' and resid 19 through 21 removed outlier: 6.391A pdb=" N SER H 20 " --> pdb=" O TYR H 107 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.616A pdb=" N ASP H 94 " --> pdb=" O LYS H 31 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.565A pdb=" N ILE H 93 " --> pdb=" O CYS H 213 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 242 through 243 Processing sheet with id=AE5, first strand: chain 'M' and resid 40 through 42 removed outlier: 3.603A pdb=" N ILE M 58 " --> pdb=" O LEU M 6 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL M 60 " --> pdb=" O GLN M 4 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS M 85 " --> pdb=" O ILE M 7 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 40 through 42 removed outlier: 3.603A pdb=" N ILE M 58 " --> pdb=" O LEU M 6 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL M 60 " --> pdb=" O GLN M 4 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 99 through 100 removed outlier: 3.583A pdb=" N ALA M 160 " --> pdb=" O LYS M 100 " (cutoff:3.500A) 853 hydrogen bonds defined for protein. 2328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 7.94 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5297 1.33 - 1.45: 5517 1.45 - 1.57: 12365 1.57 - 1.69: 192 1.69 - 1.81: 173 Bond restraints: 23544 Sorted by residual: bond pdb=" C TYR E 249 " pdb=" N LEU E 250 " ideal model delta sigma weight residual 1.330 1.431 -0.101 1.41e-02 5.03e+03 5.09e+01 bond pdb=" C LYS D 203 " pdb=" N ARG D 204 " ideal model delta sigma weight residual 1.331 1.242 0.089 1.25e-02 6.40e+03 5.06e+01 bond pdb=" C LYS H 307 " pdb=" N ASN H 308 " ideal model delta sigma weight residual 1.330 1.253 0.077 1.37e-02 5.33e+03 3.15e+01 bond pdb=" C GLU H 272 " pdb=" N PHE H 273 " ideal model delta sigma weight residual 1.335 1.255 0.079 1.42e-02 4.96e+03 3.13e+01 bond pdb=" C ARG D 204 " pdb=" N GLU D 205 " ideal model delta sigma weight residual 1.333 1.256 0.077 1.47e-02 4.63e+03 2.74e+01 ... (remaining 23539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 30864 2.46 - 4.93: 1228 4.93 - 7.39: 190 7.39 - 9.86: 52 9.86 - 12.32: 4 Bond angle restraints: 32338 Sorted by residual: angle pdb=" N GLY H 202 " pdb=" CA GLY H 202 " pdb=" C GLY H 202 " ideal model delta sigma weight residual 113.58 123.03 -9.45 1.07e+00 8.73e-01 7.79e+01 angle pdb=" N GLU M 22 " pdb=" CA GLU M 22 " pdb=" C GLU M 22 " ideal model delta sigma weight residual 110.97 119.56 -8.59 1.09e+00 8.42e-01 6.21e+01 angle pdb=" N ILE E 231 " pdb=" CA ILE E 231 " pdb=" C ILE E 231 " ideal model delta sigma weight residual 112.43 105.72 6.71 9.20e-01 1.18e+00 5.33e+01 angle pdb=" N THR G 270 " pdb=" CA THR G 270 " pdb=" C THR G 270 " ideal model delta sigma weight residual 110.50 100.24 10.26 1.41e+00 5.03e-01 5.30e+01 angle pdb=" N GLU M 79 " pdb=" CA GLU M 79 " pdb=" C GLU M 79 " ideal model delta sigma weight residual 111.34 101.20 10.14 1.49e+00 4.50e-01 4.63e+01 ... (remaining 32333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 13550 35.66 - 71.33: 548 71.33 - 106.99: 36 106.99 - 142.66: 6 142.66 - 178.32: 11 Dihedral angle restraints: 14151 sinusoidal: 6392 harmonic: 7759 Sorted by residual: dihedral pdb=" O4' U L 21 " pdb=" C1' U L 21 " pdb=" N1 U L 21 " pdb=" C2 U L 21 " ideal model delta sinusoidal sigma weight residual -160.00 -28.08 -131.92 1 1.50e+01 4.44e-03 7.12e+01 dihedral pdb=" O4' C L 34 " pdb=" C1' C L 34 " pdb=" N1 C L 34 " pdb=" C2 C L 34 " ideal model delta sinusoidal sigma weight residual -128.00 50.12 -178.12 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C L 52 " pdb=" C1' C L 52 " pdb=" N1 C L 52 " pdb=" C2 C L 52 " ideal model delta sinusoidal sigma weight residual -128.00 50.10 -178.10 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 14148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 3530 0.150 - 0.300: 114 0.300 - 0.450: 2 0.450 - 0.600: 0 0.600 - 0.750: 2 Chirality restraints: 3648 Sorted by residual: chirality pdb=" CB ILE M 57 " pdb=" CA ILE M 57 " pdb=" CG1 ILE M 57 " pdb=" CG2 ILE M 57 " both_signs ideal model delta sigma weight residual False 2.64 1.90 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CB VAL F 93 " pdb=" CA VAL F 93 " pdb=" CG1 VAL F 93 " pdb=" CG2 VAL F 93 " both_signs ideal model delta sigma weight residual False -2.63 -1.96 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CG LEU F 202 " pdb=" CB LEU F 202 " pdb=" CD1 LEU F 202 " pdb=" CD2 LEU F 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 3645 not shown) Planarity restraints: 3820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 231 " -0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ILE E 231 " 0.078 2.00e-02 2.50e+03 pdb=" O ILE E 231 " -0.030 2.00e-02 2.50e+03 pdb=" N LEU E 232 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG H 291 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO H 292 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO H 292 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO H 292 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 75 " -0.065 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO C 76 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.053 5.00e-02 4.00e+02 ... (remaining 3817 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5838 2.80 - 3.32: 18135 3.32 - 3.85: 35988 3.85 - 4.37: 43373 4.37 - 4.90: 74172 Nonbonded interactions: 177506 Sorted by model distance: nonbonded pdb=" OD1 ASN E 11 " pdb=" ND2 ASN E 104 " model vdw 2.273 3.120 nonbonded pdb=" OG1 THR D 35 " pdb=" OG1 THR D 90 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR C 35 " pdb=" OG1 THR C 90 " model vdw 2.322 3.040 nonbonded pdb=" O GLU D 278 " pdb=" OH TYR D 318 " model vdw 2.323 3.040 nonbonded pdb=" O GLU A 278 " pdb=" OH TYR A 318 " model vdw 2.325 3.040 ... (remaining 177501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 51 or resid 79 through 174 or (res \ id 175 and (name N or name CA or name C or name O or name CB )) or resid 176 thr \ ough 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) \ or resid 204 through 231 or resid 236 through 238 or (resid 239 and (name N or n \ ame CA or name C or name O or name CB )) or resid 240 through 283 or (resid 284 \ and (name N or name CA or name C or name O or name CB )) or resid 285 through 28 \ 7 or (resid 288 and (name N or name CA or name C or name O or name CB )) or resi \ d 289 through 302 or (resid 303 and (name N or name CA or name C or name O or na \ me CB )) or resid 304 through 306 or (resid 307 and (name N or name CA or name C \ or name O or name CB )) or resid 308 through 330 or (resid 331 through 332 and \ (name N or name CA or name C or name O or name CB )) or resid 333)) selection = (chain 'B' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 51 or resid 79 through 174 or (resid 175 and \ (name N or name CA or name C or name O or name CB )) or resid 176 through 202 o \ r (resid 203 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 04 through 231 or resid 236 through 283 or (resid 284 and (name N or name CA or \ name C or name O or name CB )) or resid 285 through 287 or (resid 288 and (name \ N or name CA or name C or name O or name CB )) or resid 289 through 302 or (resi \ d 303 and (name N or name CA or name C or name O or name CB )) or resid 304 thro \ ugh 306 or (resid 307 and (name N or name CA or name C or name O or name CB )) o \ r resid 308 through 330 or (resid 331 through 332 and (name N or name CA or name \ C or name O or name CB )) or resid 333)) selection = (chain 'C' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 51 or resid 79 through 174 or (resid 175 and (name N or n \ ame CA or name C or name O or name CB )) or resid 176 through 202 or (resid 203 \ and (name N or name CA or name C or name O or name CB )) or resid 204 through 23 \ 1 or resid 236 through 283 or (resid 284 and (name N or name CA or name C or nam \ e O or name CB )) or resid 285 through 287 or (resid 288 and (name N or name CA \ or name C or name O or name CB )) or resid 289 through 302 or (resid 303 and (na \ me N or name CA or name C or name O or name CB )) or resid 304 through 306 or (r \ esid 307 and (name N or name CA or name C or name O or name CB )) or resid 308 t \ hrough 330 or (resid 331 through 332 and (name N or name CA or name C or name O \ or name CB )) or resid 333)) selection = (chain 'D' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 51 or resid 79 through 174 or (resid 175 and (name N or n \ ame CA or name C or name O or name CB )) or resid 176 through 202 or (resid 203 \ and (name N or name CA or name C or name O or name CB )) or resid 204 through 23 \ 1 or resid 236 through 238 or (resid 239 and (name N or name CA or name C or nam \ e O or name CB )) or resid 240 through 283 or (resid 284 and (name N or name CA \ or name C or name O or name CB )) or resid 285 through 287 or (resid 288 and (na \ me N or name CA or name C or name O or name CB )) or resid 289 through 302 or (r \ esid 303 and (name N or name CA or name C or name O or name CB )) or resid 304 t \ hrough 330 or (resid 331 through 332 and (name N or name CA or name C or name O \ or name CB )) or resid 333)) selection = (chain 'G' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 51 or resid 79 through 174 or (resid 175 and \ (name N or name CA or name C or name O or name CB )) or resid 176 through 202 o \ r (resid 203 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 04 through 231 or resid 236 through 287 or (resid 288 and (name N or name CA or \ name C or name O or name CB )) or resid 289 through 302 or (resid 303 and (name \ N or name CA or name C or name O or name CB )) or resid 304 through 306 or (resi \ d 307 and (name N or name CA or name C or name O or name CB )) or resid 308 thro \ ugh 331 or (resid 332 and (name N or name CA or name C or name O or name CB )) o \ r resid 333)) selection = (chain 'H' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 306 or (resid 307 and (name N or name CA or name C or nam \ e O or name CB )) or resid 308 through 333)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 24.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.090 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 59.130 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 23544 Z= 0.439 Angle : 1.135 12.323 32338 Z= 0.680 Chirality : 0.066 0.750 3648 Planarity : 0.009 0.103 3820 Dihedral : 18.583 178.321 9133 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.17 % Favored : 93.53 % Rotamer: Outliers : 1.08 % Allowed : 15.70 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.14), residues: 2595 helix: -1.97 (0.15), residues: 721 sheet: 0.91 (0.26), residues: 398 loop : -2.94 (0.12), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 149 HIS 0.010 0.002 HIS H 317 PHE 0.047 0.003 PHE D 43 TYR 0.038 0.003 TYR B 138 ARG 0.016 0.001 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.23195 ( 796) hydrogen bonds : angle 7.63507 ( 2422) covalent geometry : bond 0.00726 (23544) covalent geometry : angle 1.13524 (32338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 686 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8343 (mtmm) cc_final: 0.8120 (mtpp) REVERT: A 70 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7949 (mt-10) REVERT: A 123 ASP cc_start: 0.7956 (m-30) cc_final: 0.7726 (m-30) REVERT: A 267 ASP cc_start: 0.7785 (t0) cc_final: 0.7427 (t0) REVERT: B 242 LYS cc_start: 0.8593 (mtpm) cc_final: 0.8373 (mtpm) REVERT: B 267 ASP cc_start: 0.7656 (t0) cc_final: 0.7072 (t0) REVERT: C 89 ASP cc_start: 0.8156 (p0) cc_final: 0.7930 (p0) REVERT: C 244 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7692 (mt-10) REVERT: C 314 GLU cc_start: 0.7870 (mp0) cc_final: 0.7444 (mp0) REVERT: D 61 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: D 206 TYR cc_start: 0.8172 (p90) cc_final: 0.7731 (p90) REVERT: F 57 ILE cc_start: 0.8672 (pt) cc_final: 0.8350 (pp) REVERT: F 83 ASP cc_start: 0.7326 (t70) cc_final: 0.7045 (t0) REVERT: F 85 LYS cc_start: 0.7534 (mtmt) cc_final: 0.7199 (mtmt) REVERT: F 171 TYR cc_start: 0.8349 (t80) cc_final: 0.7898 (t80) REVERT: F 260 ILE cc_start: 0.8419 (mt) cc_final: 0.8195 (mp) REVERT: F 315 ASP cc_start: 0.7923 (t0) cc_final: 0.7690 (t0) REVERT: H 37 PHE cc_start: 0.7823 (t80) cc_final: 0.7537 (t80) REVERT: H 43 PHE cc_start: 0.8754 (t80) cc_final: 0.8539 (t80) REVERT: H 186 ASN cc_start: 0.8361 (t0) cc_final: 0.7909 (t160) REVERT: H 273 PHE cc_start: 0.7982 (p90) cc_final: 0.7736 (p90) REVERT: M 1 MET cc_start: 0.6352 (mtm) cc_final: 0.5929 (pmm) REVERT: M 59 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7020 (mt-10) REVERT: M 74 GLU cc_start: 0.7460 (tt0) cc_final: 0.7149 (tt0) REVERT: M 98 LEU cc_start: 0.7147 (mm) cc_final: 0.6832 (mm) REVERT: M 105 GLU cc_start: 0.7587 (tp30) cc_final: 0.7347 (tp30) REVERT: M 109 GLU cc_start: 0.7148 (pt0) cc_final: 0.6907 (pt0) outliers start: 24 outliers final: 6 residues processed: 695 average time/residue: 1.7112 time to fit residues: 1361.2629 Evaluate side-chains 633 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 626 time to evaluate : 4.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain M residue 143 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 0.9980 chunk 203 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS B 18 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS B 279 ASN C 18 ASN C 317 HIS D 18 ASN D 140 ASN D 250 HIS E 59 HIS E 214 HIS F 47 ASN F 149 GLN F 159 HIS F 238 ASN F 270 ASN F 319 ASN G 18 ASN G 140 ASN H 80 GLN H 140 ASN H 190 ASN H 195 GLN M 53 HIS M 141 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.117498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.103072 restraints weight = 33424.247| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.61 r_work: 0.3371 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23544 Z= 0.165 Angle : 0.651 9.437 32338 Z= 0.355 Chirality : 0.045 0.245 3648 Planarity : 0.006 0.067 3820 Dihedral : 19.851 177.015 4200 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.89 % Favored : 94.91 % Rotamer: Outliers : 3.42 % Allowed : 16.78 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.15), residues: 2595 helix: -0.28 (0.18), residues: 737 sheet: 1.15 (0.26), residues: 438 loop : -2.67 (0.13), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 149 HIS 0.004 0.001 HIS E 94 PHE 0.013 0.001 PHE D 95 TYR 0.014 0.001 TYR H 271 ARG 0.007 0.001 ARG M 103 Details of bonding type rmsd hydrogen bonds : bond 0.05055 ( 796) hydrogen bonds : angle 4.86210 ( 2422) covalent geometry : bond 0.00363 (23544) covalent geometry : angle 0.65067 (32338) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 651 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 267 ASP cc_start: 0.7540 (t0) cc_final: 0.7246 (t0) REVERT: C 57 SER cc_start: 0.8391 (t) cc_final: 0.8162 (p) REVERT: C 228 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7838 (mt-10) REVERT: C 244 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7982 (mt-10) REVERT: D 206 TYR cc_start: 0.8201 (p90) cc_final: 0.7808 (p90) REVERT: D 228 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: D 242 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8478 (mtmm) REVERT: F 57 ILE cc_start: 0.8636 (pt) cc_final: 0.8364 (pp) REVERT: F 171 TYR cc_start: 0.8331 (t80) cc_final: 0.7964 (t80) REVERT: F 247 ASN cc_start: 0.8263 (m-40) cc_final: 0.8055 (t0) REVERT: F 291 LYS cc_start: 0.8296 (tttp) cc_final: 0.8094 (tttp) REVERT: F 315 ASP cc_start: 0.8017 (t0) cc_final: 0.7762 (t0) REVERT: G 93 ILE cc_start: 0.8692 (mt) cc_final: 0.8425 (tt) REVERT: G 320 MET cc_start: 0.8644 (mmt) cc_final: 0.8199 (mmt) REVERT: H 37 PHE cc_start: 0.7706 (t80) cc_final: 0.7417 (t80) REVERT: H 43 PHE cc_start: 0.8661 (t80) cc_final: 0.8449 (t80) REVERT: H 258 LEU cc_start: 0.8891 (mt) cc_final: 0.8671 (mp) REVERT: M 1 MET cc_start: 0.6580 (OUTLIER) cc_final: 0.6350 (pmm) REVERT: M 59 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7045 (mt-10) REVERT: M 74 GLU cc_start: 0.7661 (tt0) cc_final: 0.7339 (tt0) REVERT: M 98 LEU cc_start: 0.7183 (mm) cc_final: 0.6903 (mm) REVERT: M 105 GLU cc_start: 0.7412 (tp30) cc_final: 0.7197 (tp30) REVERT: M 175 LEU cc_start: 0.8138 (tp) cc_final: 0.7865 (mp) outliers start: 76 outliers final: 28 residues processed: 679 average time/residue: 1.3787 time to fit residues: 1066.5195 Evaluate side-chains 641 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 611 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain M residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 147 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 134 optimal weight: 0.0870 chunk 236 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN C 18 ASN D 18 ASN D 140 ASN E 52 ASN F 82 ASN F 149 GLN F 159 HIS F 270 ASN G 178 ASN G 252 GLN H 186 ASN H 195 GLN ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.115727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101189 restraints weight = 33433.320| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.61 r_work: 0.3342 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23544 Z= 0.176 Angle : 0.602 9.146 32338 Z= 0.327 Chirality : 0.044 0.236 3648 Planarity : 0.005 0.058 3820 Dihedral : 19.568 177.593 4190 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.64 % Allowed : 17.86 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 2595 helix: 0.49 (0.19), residues: 739 sheet: 1.15 (0.26), residues: 450 loop : -2.50 (0.13), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 149 HIS 0.005 0.001 HIS E 59 PHE 0.028 0.002 PHE H 273 TYR 0.023 0.001 TYR H 125 ARG 0.006 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.05294 ( 796) hydrogen bonds : angle 4.56484 ( 2422) covalent geometry : bond 0.00411 (23544) covalent geometry : angle 0.60202 (32338) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 633 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 TYR cc_start: 0.8469 (p90) cc_final: 0.8044 (p90) REVERT: B 241 PHE cc_start: 0.8729 (t80) cc_final: 0.8461 (t80) REVERT: B 267 ASP cc_start: 0.7597 (t0) cc_final: 0.7278 (t0) REVERT: D 206 TYR cc_start: 0.7910 (p90) cc_final: 0.7638 (p90) REVERT: D 228 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: F 57 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8406 (pp) REVERT: F 171 TYR cc_start: 0.8465 (t80) cc_final: 0.8197 (t80) REVERT: F 247 ASN cc_start: 0.8416 (m-40) cc_final: 0.8192 (t0) REVERT: F 272 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7977 (mtt180) REVERT: F 277 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7254 (mtp85) REVERT: F 291 LYS cc_start: 0.8345 (tttp) cc_final: 0.8129 (tttp) REVERT: F 315 ASP cc_start: 0.7994 (t0) cc_final: 0.7743 (t0) REVERT: F 320 MET cc_start: 0.8613 (mtp) cc_final: 0.8387 (mtp) REVERT: H 37 PHE cc_start: 0.7699 (t80) cc_final: 0.7375 (t80) REVERT: M 1 MET cc_start: 0.6770 (mtm) cc_final: 0.6558 (pmm) REVERT: M 59 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7031 (mt-10) REVERT: M 74 GLU cc_start: 0.7579 (tt0) cc_final: 0.7252 (tt0) REVERT: M 98 LEU cc_start: 0.7313 (mm) cc_final: 0.7093 (mm) REVERT: M 105 GLU cc_start: 0.7470 (tp30) cc_final: 0.7171 (tp30) REVERT: M 106 ASN cc_start: 0.8389 (t0) cc_final: 0.7903 (m-40) REVERT: M 109 GLU cc_start: 0.7421 (pt0) cc_final: 0.7178 (pt0) outliers start: 81 outliers final: 33 residues processed: 662 average time/residue: 1.3589 time to fit residues: 1024.9411 Evaluate side-chains 648 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 612 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 277 ARG Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 116 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 97 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN B 80 GLN B 140 ASN B 308 ASN C 308 ASN D 144 ASN E 52 ASN F 82 ASN F 149 GLN F 159 HIS G 140 ASN G 178 ASN G 252 GLN H 18 ASN H 80 GLN H 186 ASN H 195 GLN H 252 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.115938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.101387 restraints weight = 33835.548| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.61 r_work: 0.3344 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23544 Z= 0.153 Angle : 0.571 9.217 32338 Z= 0.310 Chirality : 0.043 0.221 3648 Planarity : 0.005 0.054 3820 Dihedral : 19.463 177.301 4188 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.24 % Allowed : 18.80 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2595 helix: 0.89 (0.20), residues: 740 sheet: 1.13 (0.25), residues: 473 loop : -2.41 (0.13), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 149 HIS 0.005 0.001 HIS E 59 PHE 0.024 0.001 PHE H 273 TYR 0.015 0.001 TYR H 271 ARG 0.008 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 796) hydrogen bonds : angle 4.40264 ( 2422) covalent geometry : bond 0.00356 (23544) covalent geometry : angle 0.57102 (32338) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 611 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8591 (mtpp) cc_final: 0.8352 (mtpp) REVERT: B 206 TYR cc_start: 0.8508 (p90) cc_final: 0.8102 (p90) REVERT: B 229 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7540 (ttp) REVERT: C 191 GLU cc_start: 0.7772 (pt0) cc_final: 0.7560 (pt0) REVERT: D 228 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: F 57 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8414 (pp) REVERT: F 171 TYR cc_start: 0.8479 (t80) cc_final: 0.8251 (t80) REVERT: F 247 ASN cc_start: 0.8391 (m-40) cc_final: 0.8178 (t0) REVERT: F 277 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7272 (mtp85) REVERT: F 291 LYS cc_start: 0.8324 (tttp) cc_final: 0.8019 (tttp) REVERT: F 315 ASP cc_start: 0.7985 (t0) cc_final: 0.7692 (t0) REVERT: F 320 MET cc_start: 0.8606 (mtp) cc_final: 0.8388 (mtp) REVERT: G 89 ASP cc_start: 0.8078 (p0) cc_final: 0.7849 (p0) REVERT: H 37 PHE cc_start: 0.7668 (t80) cc_final: 0.7381 (t80) REVERT: H 290 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7299 (m-10) REVERT: M 74 GLU cc_start: 0.7523 (tt0) cc_final: 0.7207 (tt0) REVERT: M 109 GLU cc_start: 0.7408 (pt0) cc_final: 0.7088 (pt0) outliers start: 72 outliers final: 43 residues processed: 635 average time/residue: 1.4177 time to fit residues: 1023.7812 Evaluate side-chains 651 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 603 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 277 ARG Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 116 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 77 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 193 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN D 18 ASN D 140 ASN D 144 ASN E 52 ASN F 71 ASN F 149 GLN F 159 HIS G 140 ASN G 178 ASN G 252 GLN G 256 ASN H 18 ASN H 178 ASN H 186 ASN H 195 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.116371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101736 restraints weight = 33677.414| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.64 r_work: 0.3348 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23544 Z= 0.137 Angle : 0.556 9.218 32338 Z= 0.300 Chirality : 0.042 0.205 3648 Planarity : 0.005 0.050 3820 Dihedral : 19.392 177.237 4188 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.33 % Allowed : 19.43 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.16), residues: 2595 helix: 1.15 (0.20), residues: 739 sheet: 1.19 (0.25), residues: 467 loop : -2.31 (0.13), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 149 HIS 0.005 0.001 HIS E 59 PHE 0.023 0.001 PHE H 273 TYR 0.014 0.001 TYR G 265 ARG 0.008 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 796) hydrogen bonds : angle 4.24890 ( 2422) covalent geometry : bond 0.00314 (23544) covalent geometry : angle 0.55583 (32338) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 619 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 229 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7530 (ttp) REVERT: C 71 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8137 (mm) REVERT: D 228 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: D 284 ARG cc_start: 0.7591 (ttm170) cc_final: 0.7325 (ttm170) REVERT: F 57 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8416 (pp) REVERT: F 247 ASN cc_start: 0.8401 (m-40) cc_final: 0.8200 (t0) REVERT: F 277 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7376 (mtp85) REVERT: F 291 LYS cc_start: 0.8342 (tttp) cc_final: 0.8002 (tttp) REVERT: F 315 ASP cc_start: 0.7960 (t0) cc_final: 0.7673 (t0) REVERT: F 320 MET cc_start: 0.8595 (mtp) cc_final: 0.8383 (mtp) REVERT: H 37 PHE cc_start: 0.7645 (t80) cc_final: 0.7352 (t80) REVERT: H 290 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7299 (m-10) REVERT: M 74 GLU cc_start: 0.7499 (tt0) cc_final: 0.7216 (tt0) REVERT: M 109 GLU cc_start: 0.7440 (pt0) cc_final: 0.7077 (pt0) outliers start: 74 outliers final: 39 residues processed: 641 average time/residue: 1.4032 time to fit residues: 1022.5280 Evaluate side-chains 655 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 610 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 277 ARG Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 61 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 232 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 257 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 231 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN B 80 GLN B 140 ASN D 18 ASN D 140 ASN D 144 ASN E 52 ASN F 71 ASN F 149 GLN F 159 HIS G 140 ASN G 252 GLN H 18 ASN H 80 GLN H 178 ASN H 186 ASN H 195 GLN H 256 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.113692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.099022 restraints weight = 33326.277| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.61 r_work: 0.3307 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 23544 Z= 0.253 Angle : 0.621 9.409 32338 Z= 0.335 Chirality : 0.046 0.305 3648 Planarity : 0.005 0.052 3820 Dihedral : 19.352 178.612 4188 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.51 % Allowed : 19.34 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2595 helix: 1.06 (0.20), residues: 740 sheet: 1.09 (0.25), residues: 463 loop : -2.33 (0.13), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 149 HIS 0.006 0.001 HIS E 59 PHE 0.034 0.002 PHE H 43 TYR 0.019 0.002 TYR A 271 ARG 0.010 0.001 ARG D 284 Details of bonding type rmsd hydrogen bonds : bond 0.05628 ( 796) hydrogen bonds : angle 4.45562 ( 2422) covalent geometry : bond 0.00615 (23544) covalent geometry : angle 0.62064 (32338) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 630 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 71 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8226 (mm) REVERT: D 228 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: F 57 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8427 (pp) REVERT: F 247 ASN cc_start: 0.8500 (m-40) cc_final: 0.8155 (t0) REVERT: F 277 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7383 (mtp85) REVERT: F 291 LYS cc_start: 0.8359 (tttp) cc_final: 0.8023 (tttp) REVERT: F 315 ASP cc_start: 0.7967 (t0) cc_final: 0.7682 (t0) REVERT: F 320 MET cc_start: 0.8621 (mtp) cc_final: 0.8399 (mtp) REVERT: H 37 PHE cc_start: 0.7769 (t80) cc_final: 0.7479 (t80) REVERT: H 124 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7661 (mt-10) REVERT: H 290 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7461 (m-10) REVERT: H 315 ASP cc_start: 0.6975 (m-30) cc_final: 0.6731 (m-30) REVERT: M 74 GLU cc_start: 0.7526 (tt0) cc_final: 0.7247 (tt0) REVERT: M 106 ASN cc_start: 0.8454 (m110) cc_final: 0.8231 (m-40) REVERT: M 109 GLU cc_start: 0.7535 (pt0) cc_final: 0.7166 (pt0) outliers start: 78 outliers final: 48 residues processed: 655 average time/residue: 1.4329 time to fit residues: 1064.9951 Evaluate side-chains 670 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 617 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 277 ARG Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 116 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 267 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 181 optimal weight: 0.0870 chunk 117 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN B 140 ASN C 308 ASN D 18 ASN D 80 GLN D 144 ASN F 71 ASN F 159 HIS G 140 ASN G 252 GLN H 18 ASN H 80 GLN H 186 ASN H 195 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.117165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.102403 restraints weight = 33695.538| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.62 r_work: 0.3359 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23544 Z= 0.115 Angle : 0.546 9.303 32338 Z= 0.295 Chirality : 0.042 0.275 3648 Planarity : 0.005 0.049 3820 Dihedral : 19.253 177.838 4188 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.24 % Allowed : 20.38 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2595 helix: 1.32 (0.20), residues: 738 sheet: 1.14 (0.25), residues: 468 loop : -2.21 (0.14), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 149 HIS 0.004 0.001 HIS A 317 PHE 0.026 0.001 PHE D 43 TYR 0.014 0.001 TYR G 265 ARG 0.010 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 796) hydrogen bonds : angle 4.09462 ( 2422) covalent geometry : bond 0.00259 (23544) covalent geometry : angle 0.54608 (32338) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 622 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 71 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8176 (mm) REVERT: D 228 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: F 57 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8435 (pp) REVERT: F 247 ASN cc_start: 0.8497 (m-40) cc_final: 0.8279 (t0) REVERT: F 291 LYS cc_start: 0.8350 (tttp) cc_final: 0.8015 (tttp) REVERT: F 315 ASP cc_start: 0.7955 (t0) cc_final: 0.7636 (t0) REVERT: F 320 MET cc_start: 0.8638 (mtp) cc_final: 0.8404 (mtp) REVERT: H 37 PHE cc_start: 0.7602 (t80) cc_final: 0.7327 (t80) REVERT: H 124 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7563 (mt-10) REVERT: H 290 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7414 (m-10) REVERT: H 315 ASP cc_start: 0.6809 (m-30) cc_final: 0.6576 (m-30) REVERT: M 74 GLU cc_start: 0.7489 (tt0) cc_final: 0.7210 (tt0) REVERT: M 106 ASN cc_start: 0.8401 (m110) cc_final: 0.8201 (m-40) REVERT: M 109 GLU cc_start: 0.7535 (pt0) cc_final: 0.7160 (pt0) outliers start: 72 outliers final: 35 residues processed: 641 average time/residue: 1.4887 time to fit residues: 1085.1499 Evaluate side-chains 654 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 615 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 90 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 129 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 0.0670 chunk 93 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN B 80 GLN D 18 ASN D 144 ASN E 52 ASN F 71 ASN F 139 GLN F 149 GLN F 159 HIS G 140 ASN G 252 GLN H 18 ASN H 80 GLN H 178 ASN H 186 ASN H 195 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.113800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.099064 restraints weight = 33290.757| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.61 r_work: 0.3308 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 23544 Z= 0.233 Angle : 0.613 9.565 32338 Z= 0.330 Chirality : 0.046 0.292 3648 Planarity : 0.005 0.054 3820 Dihedral : 19.204 178.682 4187 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.28 % Allowed : 20.65 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.16), residues: 2595 helix: 1.20 (0.20), residues: 739 sheet: 1.03 (0.25), residues: 463 loop : -2.22 (0.14), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 149 HIS 0.006 0.001 HIS E 59 PHE 0.044 0.002 PHE H 43 TYR 0.018 0.002 TYR H 265 ARG 0.009 0.001 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.05510 ( 796) hydrogen bonds : angle 4.37759 ( 2422) covalent geometry : bond 0.00562 (23544) covalent geometry : angle 0.61311 (32338) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 611 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 71 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8262 (mm) REVERT: D 228 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: F 57 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8434 (pp) REVERT: F 247 ASN cc_start: 0.8522 (m-40) cc_final: 0.8175 (t0) REVERT: F 291 LYS cc_start: 0.8360 (tttp) cc_final: 0.8037 (tttp) REVERT: F 315 ASP cc_start: 0.7961 (t0) cc_final: 0.7651 (t0) REVERT: F 320 MET cc_start: 0.8650 (mtp) cc_final: 0.8429 (mtp) REVERT: G 121 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8491 (mptt) REVERT: G 165 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7921 (mm-30) REVERT: H 37 PHE cc_start: 0.7775 (t80) cc_final: 0.7457 (t80) REVERT: H 290 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7530 (m-10) REVERT: H 315 ASP cc_start: 0.6958 (m-30) cc_final: 0.6715 (m-30) REVERT: M 74 GLU cc_start: 0.7532 (tt0) cc_final: 0.7249 (tt0) REVERT: M 106 ASN cc_start: 0.8473 (m110) cc_final: 0.8222 (m110) REVERT: M 109 GLU cc_start: 0.7571 (pt0) cc_final: 0.7191 (pt0) outliers start: 73 outliers final: 42 residues processed: 631 average time/residue: 1.4538 time to fit residues: 1038.4688 Evaluate side-chains 654 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 607 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 98 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 102 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN D 18 ASN D 144 ASN F 35 HIS F 71 ASN F 159 HIS G 140 ASN G 252 GLN H 18 ASN H 80 GLN H 178 ASN H 186 ASN H 195 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.115993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101220 restraints weight = 33515.739| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.62 r_work: 0.3341 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23544 Z= 0.135 Angle : 0.558 9.326 32338 Z= 0.301 Chirality : 0.042 0.200 3648 Planarity : 0.005 0.054 3820 Dihedral : 19.105 179.105 4187 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.43 % Allowed : 21.59 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2595 helix: 1.32 (0.20), residues: 738 sheet: 1.11 (0.25), residues: 462 loop : -2.14 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 149 HIS 0.004 0.001 HIS E 59 PHE 0.049 0.001 PHE H 43 TYR 0.020 0.001 TYR H 125 ARG 0.008 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 796) hydrogen bonds : angle 4.15303 ( 2422) covalent geometry : bond 0.00313 (23544) covalent geometry : angle 0.55811 (32338) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 598 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 221 MET cc_start: 0.8790 (mmt) cc_final: 0.8376 (mmt) REVERT: D 228 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: F 57 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8444 (pp) REVERT: F 247 ASN cc_start: 0.8519 (m-40) cc_final: 0.8156 (t0) REVERT: F 291 LYS cc_start: 0.8324 (tttp) cc_final: 0.7995 (tttp) REVERT: F 315 ASP cc_start: 0.7948 (t0) cc_final: 0.7609 (t0) REVERT: F 320 MET cc_start: 0.8648 (mtp) cc_final: 0.8410 (mtp) REVERT: G 165 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7899 (mm-30) REVERT: H 37 PHE cc_start: 0.7662 (t80) cc_final: 0.7359 (t80) REVERT: H 290 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7484 (m-10) REVERT: H 315 ASP cc_start: 0.6846 (m-30) cc_final: 0.6599 (m-30) REVERT: M 74 GLU cc_start: 0.7512 (tt0) cc_final: 0.7218 (tt0) REVERT: M 106 ASN cc_start: 0.8458 (m110) cc_final: 0.8239 (m-40) REVERT: M 109 GLU cc_start: 0.7562 (pt0) cc_final: 0.7187 (pt0) outliers start: 54 outliers final: 35 residues processed: 615 average time/residue: 1.4631 time to fit residues: 1019.9377 Evaluate side-chains 633 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 595 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 176 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 163 optimal weight: 0.0870 chunk 165 optimal weight: 0.2980 chunk 192 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 125 optimal weight: 0.4980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN D 18 ASN D 144 ASN F 71 ASN F 149 GLN F 159 HIS F 335 HIS G 140 ASN G 252 GLN H 18 ASN H 178 ASN H 186 ASN H 195 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.117411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.102641 restraints weight = 33644.356| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.62 r_work: 0.3363 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23544 Z= 0.115 Angle : 0.537 9.465 32338 Z= 0.288 Chirality : 0.041 0.191 3648 Planarity : 0.005 0.052 3820 Dihedral : 18.994 179.314 4187 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.11 % Allowed : 22.13 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2595 helix: 1.43 (0.20), residues: 743 sheet: 1.05 (0.25), residues: 480 loop : -2.08 (0.14), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 149 HIS 0.005 0.001 HIS E 59 PHE 0.040 0.001 PHE H 43 TYR 0.027 0.001 TYR H 125 ARG 0.009 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 796) hydrogen bonds : angle 4.01057 ( 2422) covalent geometry : bond 0.00261 (23544) covalent geometry : angle 0.53673 (32338) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 606 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 221 MET cc_start: 0.8833 (mmt) cc_final: 0.8414 (mmt) REVERT: D 228 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: F 57 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8464 (pp) REVERT: F 291 LYS cc_start: 0.8308 (tttp) cc_final: 0.7966 (tttp) REVERT: F 315 ASP cc_start: 0.7930 (t0) cc_final: 0.7580 (t0) REVERT: F 320 MET cc_start: 0.8624 (mtp) cc_final: 0.8396 (mtp) REVERT: G 165 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7844 (mm-30) REVERT: G 309 GLU cc_start: 0.7820 (tt0) cc_final: 0.7581 (mt-10) REVERT: H 290 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7517 (m-10) REVERT: H 315 ASP cc_start: 0.6756 (m-30) cc_final: 0.6512 (m-30) REVERT: M 74 GLU cc_start: 0.7504 (tt0) cc_final: 0.7214 (tt0) REVERT: M 106 ASN cc_start: 0.8419 (m110) cc_final: 0.8197 (m-40) REVERT: M 109 GLU cc_start: 0.7535 (pt0) cc_final: 0.7136 (pt0) outliers start: 47 outliers final: 32 residues processed: 616 average time/residue: 1.5203 time to fit residues: 1068.9637 Evaluate side-chains 634 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 599 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 95 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 239 optimal weight: 0.0270 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 208 ASN A 252 GLN B 18 ASN B 75 ASN B 144 ASN D 18 ASN D 144 ASN E 59 HIS ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN F 149 GLN F 159 HIS F 247 ASN G 252 GLN H 18 ASN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 ASN H 186 ASN H 195 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.117392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.102623 restraints weight = 33588.122| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.62 r_work: 0.3364 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 23544 Z= 0.149 Angle : 0.703 59.196 32338 Z= 0.410 Chirality : 0.042 0.300 3648 Planarity : 0.005 0.053 3820 Dihedral : 18.993 179.316 4187 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.02 % Allowed : 22.72 % Favored : 75.26 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2595 helix: 1.41 (0.20), residues: 743 sheet: 1.06 (0.25), residues: 480 loop : -2.08 (0.14), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 149 HIS 0.004 0.001 HIS E 59 PHE 0.023 0.001 PHE H 43 TYR 0.022 0.001 TYR H 125 ARG 0.007 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 796) hydrogen bonds : angle 4.02008 ( 2422) covalent geometry : bond 0.00317 (23544) covalent geometry : angle 0.70250 (32338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24918.91 seconds wall clock time: 427 minutes 55.71 seconds (25675.71 seconds total)